AIMC Topic: Mutation

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Identification of novel Xanthomonas euvesicatoria type III effector proteins by a machine-learning approach.

Molecular plant pathology Aug 15, 2015
The Gram-negative bacterium Xanthomonas euvesicatoria (Xcv) is the causal agent of bacterial spot disease in pepper and tomato. Xcv pathogenicity depends on a type III secretion (T3S) system that delivers effector proteins into host cells to suppress...
Protein Transport Xanthomonas Capsicum Bacterial Proteins Mutation Plant Diseases Plant Cells Nicotiana Bacterial Secretion Systems Base Composition Machine Learning Phylogeny Plant Leaves
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A mutation profile for top-k patient search exploiting Gene-Ontology and orthogonal non-negative matrix factorization.

Bioinformatics (Oxford, England) Jul 23, 2015
MOTIVATION: As the quantity of genomic mutation data increases, the likelihood of finding patients with similar genomic profiles, for various disease inferences, increases. However, so does the difficulty in identifying them. Similarity search based ...
Survival Analysis Chi-Square Distribution Gene Ontology Reproducibility of Results Neoplasms Mutation Humans Algorithms
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Identification of genomic features in the classification of loss- and gain-of-function mutation.

BMC medical informatics and decision making May 20, 2015
BACKGROUND: Alterations of a genome can lead to changes in protein functions. Through these genetic mutations, a protein can lose its native function (loss-of-function, LoF), or it can confer a new function (gain-of-function, GoF). However, when a mu...
Mutation Humans Data Mining Machine Learning Genomics
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Evaluation and integration of cancer gene classifiers: identification and ranking of plausible drivers.

Scientific reports May 11, 2015
The number of mutated genes in cancer cells is far larger than the number of mutations that drive cancer. The difficulty this creates for identifying relevant alterations has stimulated the development of various computational approaches to distingui...
Genes, Neoplasm Humans Machine Learning Animals Neoplasm Proteins United States Mutation Databases, Genetic
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Disentangling multidimensional spatio-temporal data into their common and aberrant responses.

PloS one Apr 22, 2015
With the advent of high-throughput measurement techniques, scientists and engineers are starting to grapple with massive data sets and encountering challenges with how to organize, process and extract information into meaningful structures. Multidime...
Proto-Oncogene Proteins c-akt Protein Array Analysis Neural Networks, Computer Quinazolines Algorithms Gene Expression Regulation, Neoplastic Female Principal Component Analysis Mutation Breast Neoplasms Lapatinib Biomarkers, Tumor Gene Regulatory Networks Humans
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Improved feature-based prediction of SNPs in human cytochrome P450 enzymes.

Interdisciplinary sciences, computational life sciences Mar 21, 2015
Single nucleotide polymorphisms (SNPs) make up the most common form of mutations in human cytochrome P450 enzymes family, and have the potential to bring with different drug responses or specific diseases in individual patients. Here, based on machin...
Phylogeny Polymorphism, Single Nucleotide Computational Biology Area Under Curve Models, Molecular Support Vector Machine Fuzzy Logic Humans Artificial Intelligence Cytochrome P-450 Enzyme System Mutation Base Sequence Amino Acids Codon Amino Acid Sequence
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Lung cancer prediction using neural network ensemble with histogram of oriented gradient genomic features.

TheScientificWorldJournal Feb 23, 2015
This paper reports an experimental comparison of artificial neural network (ANN) and support vector machine (SVM) ensembles and their "nonensemble" variants for lung cancer prediction. These machine learning classifiers were trained to predict lung c...
Proto-Oncogene Proteins p21(ras) Biomarkers, Tumor Lung Neoplasms Support Vector Machine Mutation Carcinoma, Non-Small-Cell Lung Tumor Suppressor Protein p53 ErbB Receptors Humans Neural Networks, Computer
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Deep Learning-Based Classification of NSCLC-Derived Extracellular Vesicles Using AFM Nanomechanical Signatures.

Analytical chemistry Jul 22, 2025
Nonsmall cell lung cancer (NSCLC) remains a leading cause of cancer-related mortality, with liquid biopsy emerging as a promising tool for noninvasive diagnostics. Extracellular vesicles (EVs) serve as molecular messengers of the tumor microenvironme...
Humans Extracellular Vesicles Carcinoma, Non-Small-Cell Lung Mutation Microscopy, Atomic Force Deep Learning Cell Line, Tumor Lung Neoplasms
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HawkDock version 2: an updated web server to predict and analyze the structures of protein-protein complexes.

Nucleic acids research Jul 7, 2025
Protein-protein interactions (PPIs) are fundamental to cellular functions, yet predicting and analyzing their 3D structures remains a critical and computationally demanding challenge. To address this, the HawkDock web server was developed as an integ...
Software Molecular Docking Simulation Deep Learning Protein Interaction Mapping Mutation Multiprotein Complexes Internet Protein Conformation Protein Binding Computational Biology Proteins
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StructMAn 2.0 Web: a web server for structural annotation of protein sequences and mutations.

Nucleic acids research Jul 7, 2025
StructMAn is a method for protein structural annotation. It describes each position of a protein sequence or specific variants in it in terms of their importance for the three-dimensional (3D) structure of the protein and its interactions with other ...
Molecular Sequence Annotation Sequence Analysis, Protein Internet Amino Acid Sequence Protein Conformation Software Models, Molecular User-Computer Interface Mutation Proteins
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